rdkit-devel

[Rdkit-devel] Pharm2D -- 4-point pharmacophores

[Ondrej M. <mit...@gm...>]

Hello,
I'd like to implement four-point (or generally N-point) pharmacophores 
into rdkit's  Pharm2D module. It seems that same parts of the module can 
support more-than-three-point pharmacophores without any modification, 
while some other can't. Is there any more thorough documentation than 
the one generated by epydoc which could help me uderstand how the 
generation of 2D pharmacophore fingerprints works?
Thanks,
Ondrej

Re: [Rdkit-devel] Pharm2D -- 4-point pharmacophores

[Greg L. <gre...@gm...>]

Hi Ondrej,

There's an illustration of the representation here:
http://rdkit.org/docs/RDKit_Book.html#representation-of-pharmacophore-fingerprints
Some discussion in the code of the terminology used:
https://github.com/rdkit/rdkit/blob/master/rdkit/Chem/Pharm2D/Generate.py#L11
and an illustration of the way the distances are defined:
https://github.com/rdkit/rdkit/blob/master/Docs/Code/Chem/Pharm2D.triangles.jpg

It's been a while since I really looked at that code, but I don'd think
there's really any reason why support for more than 3 features couldn't be
enabled.

-greg


On Tue, Feb 9, 2016 at 10:02 PM, Ondrej Micka <mit...@gm...> wrote:

> Hello,
> I'd like to implement four-point (or generally N-point) pharmacophores
> into rdkit's  Pharm2D module. It seems that same parts of the module can
> support more-than-three-point pharmacophores without any modification,
> while some other can't. Is there any more thorough documentation than
> the one generated by epydoc which could help me uderstand how the
> generation of 2D pharmacophore fingerprints works?
> Thanks,
> Ondrej
>
>
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Re: [Rdkit-devel] Pharm2D -- 4-point pharmacophores

[Ondrej M. <mit...@gm...>]

Hi Greg,

> There's an illustration of the representation here:
> http://rdkit.org/docs/RDKit_Book.html#representation-of-pharmacophore-fingerprints
> Some discussion in the code of the terminology used:
> https://github.com/rdkit/rdkit/blob/master/rdkit/Chem/Pharm2D/Generate.py#L11
> and an illustration of the way the distances are defined:
> https://github.com/rdkit/rdkit/blob/master/Docs/Code/Chem/Pharm2D.triangles.jpg

thank you, but I found these myself, I was looking for something more 
thorough, since the code isn't quite self-explanatory.

> It's been a while since I really looked at that code, but I don'd think
> there's really any reason why support for more than 3 features couldn't
> be enabled.

So far, I've found this line
https://github.com/rdkit/rdkit/blob/master/rdkit/Chem/Pharm2D/SigFactory.py#L231
which might be the problem when using n >= 4, but I have absolutely no 
idea, why is it there. Any suggestions?
Ondrej